Karunaratne, Oshada Fernando fifties ensure series ends at 0-0 after both Tests ended up drawn.
Brathwaite, Mayers, Holder of half-centuries helped West Indies reach 280 for 4 before declaring late on day four with a 376-run lead.
Only 42.1 overs played in the third day, they reduced visitors to 250 for 8 at stump before rain returned.
Suranga Lakmal took 4-94 but the Brathwaite century and Cornwall 73 kept the home team strong.
Every Sri Lankan bowler took a wicket, with Lakmal leading the way with three end day one of the second Test on equal footing.
England and West Indies expand the number of matches to be played in the Caribbean in 2022.
